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Omid Khalouei | 1 Mar 2006 02:18
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[BioPython] Homology Modeling question

Hello,

My question is not specifically related to Biopython, I wanted to know if 
homology modeling can be used reliably to see the effects of single amino 
acid substitutions. I mean is homoloy modeling useful for predicting the 
structure of those sequences for which there is no know structure or can it 
also be used for a more "fine tuning" analysis such as changing one amino 
acid on a PDB structure and then performing homology modeling using that 
same PDB structure as template?
Also is there any uptodate forum for homology modeling? I looked it up on 
Google but postings were for back in 1990's.

Thanks for your help.
Omid K.

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ziemys | 3 Mar 2006 21:09
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[BioPython] Bio.PDB.ResidueDepth

HI,

What sphere radius is used to calculate the surface in Bio.PDB.ResidueDepth? 1.4 ? Can the radius be
modified and how ? 

Is it needed just 'msms.exe' or I need 'pdb_to_xyzr.exe' also to install?

With best
Arturas

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Peter (BioPython | 4 Mar 2006 11:08
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Re: [BioPython] Homology Modeling question

Omid Khalouei wrote:
> Hello,
> 
> My question is not specifically related to Biopython, I wanted to know 
> if homology modeling can be used reliably to see the effects of single 
> amino acid substitutions. I mean is homoloy modeling useful for 
> predicting the structure of those sequences for which there is no know 
> structure or can it also be used for a more "fine tuning" analysis such 
> as changing one amino acid on a PDB structure and then performing 
> homology modeling using that same PDB structure as template?

I was under the impression that for homology modelling you provide an 
alignment of your sequence with several other sequences with associated 
known structures.  Have you looked at the Sali Lab's program MODELLER:

http://salilab.org/modeller/

For the simple case of "fine tuning" analysis with a single amino acid 
substitute, homology modelling might be overkill.  A simple substitution 
using the same backbone positions and initial direction for the side 
chain, followed by a molecular dynamics energy minimization of the side 
chain may be enough.  This particular question has cropped before on the 
MMTK mailing lists - MMTK is a python molecular dynamics library:

http://starship.python.net/crew/hinsen/MMTK/index.html
http://starship.python.net/pipermail/mmtk/

> Also is there any uptodate forum for homology modeling? I looked it up 
> on Google but postings were for back in 1990's.
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Michiel De Hoon | 4 Mar 2006 21:33
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RE: [BioPython] qblast fails on parsing XML results

Fixed in CVS using urllib2. Thanks to Alexander Morgan for providing the
code. Please let us know if there is still a problem with qblast.

--Michiel.

Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032

-----Original Message-----
From: biopython-bounces <at> portal.open-bio.org on behalf of Ilya Soifer
Sent: Mon 2/27/2006 10:38 AM
To: biopython <at> biopython.org
Subject: [BioPython] qblast fails on parsing XML results

Hi,
I hope that I send it to the correct list.
When I run qblast I get

>>> res1 = NCBIWWW.qblast("blastn", "nr", seq1)

Traceback (most recent call last):
 File "<pyshell#24>", line 1, in -toplevel-
   res1 = NCBIWWW.qblast("blastn", "nr", seq1)
 File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIWWW.py", line
1130, in qblast
   i = results.index("Connection: close")
ValueError: substring not found
(Continue reading)

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Kael Fischer | 7 Mar 2006 21:07
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[BioPython] Re: GenBank RecordParser Failure

That snippet is useable if you moe it down a few lines-

right after:

consumer.reference_num(data[:data.find(' ')])

and before:
consumer.reference_bases(data[data.find(' ')+1:])

-Kael

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ziemys | 7 Mar 2006 22:38
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[BioPython] HSE (half-sphere exposure)

Hi

Can anybody give more details about how to use HSE in BioPython ?

(BioPython is very nice, but at the same it suffers from the lack of documentations...)

With best
Arturas

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Thomas Hamelryck | 7 Mar 2006 22:50
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Re: [BioPython] HSE (half-sphere exposure)


On Tue, March 7, 2006 10:38 pm, ziemys <at> ecr6.ohio-state.edu wrote:
> Hi
>
>
> Can anybody give more details about how to use HSE in BioPython ?
>
>
> (BioPython is very nice, but at the same it suffers from the lack of
> documentations...)
>
> With best
> Arturas
>

Hi Arturas,

Below is an example.
Note that HSE-alpha is undefined for the first and last
residues of a polypeptide.

Best regards,

-Thomas

----

from Bio.PDB import *
import sys
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Kael Fischer | 7 Mar 2006 22:55
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[BioPython] GenBank RecordParser Failure (split REFERENCE line)

I sent this earlier but I don't think it got through.  I was using a
diffreent email address.  Sorry if this is a duplicate.

Using the  Bio/GenBank/__init__.py from the CVS HEAD (v1.58), parsing of:
J01917.1  GI:209811 fails.

The file pointer is at the end of the record and the traceback is:

Traceback (most recent call last):
  File "gb2fasta.py", line 21, in ?
    for gbr in GenBank.Iterator(f,parser=gbParser):
  File "/usr/local/lib/python2.4/site-packages/Bio/GenBank/__init__.py",
line 146, in next
    return self._parser.parse( File.StringHandle(data))
  File "/usr/local/lib/python2.4/site-packages/Bio/GenBank/__init__.py",
line 212, in parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/local/lib/python2.4/site-packages/Bio/GenBank/__init__.py",
line 1518, in feed
    line = self._feed_header(handle, consumer)
  File "/usr/local/lib/python2.4/site-packages/Bio/GenBank/__init__.py",
line 1386, in _feed_header
    assert line[0:GENBANK_INDENT] <> GENBANK_SPACER, \
AssertionError: Unexpected continuation of an entry:
            28259)

The _feed_header method does not deal with REFERENCE ... (bases ....) being
split across lines.

A diff which fixes __init__.py is attached.  It appears to be robust. I just
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Peter (BioPython List | 10 Mar 2006 15:07
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[BioPython] Translating ambiguous stop codons

I've been working on simple gene finding within sequence contigs from 
unfinished genomes.  Very simply I have used biopython to scan each of 
the six frames looking for a start codon, translating until the next 
stop codon - and repeating.  This is a pretty simple way of generating a 
list of possible open reading frames for further analysis.

Unfortunately (as is probably the case for many unfinished genomes) 
there are some ambiguous codons which could code for an amino acid or a 
stop codon:

e.g.
"NAG" could be E, K, Q or a stop codon
"YAG" could be either Q or a stop codon (as Y = C or T)

For example, If I have the ambiguous sequence 
"CAAGGCGTCGAAYAGCTTCAGGAACAGGAC" and try and translate it I get an 
exception, "TranslationError: YAG"

from Bio.Seq import Seq
from Bio import Translate
my_translator = Translate.ambiguous_dna_by_id[11]
my_dna = Seq('CAAGGCGTCGAAYAGCTTCAGGAACAGGAC', \
              my_translator.table.nucleotide_alphabet)

#print my_translator.translate_to_stop(my_dna)
print my_translator.translate(my_dna)

The possible translations are 'QGVEQLQEQD', and 'QGVE*LQEQD'

Is this situation something many other BioPython users have had to deal
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Michiel De Hoon | 18 Mar 2006 21:40
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[BioPython] Test - please ignore

Just testing if I can send to this mailing list. One of our users complained
that his messages were getting bounced, although he is a member of this
mailing list.

--Michiel.

Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032

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Gmane